I would highly recommend using nextflow or some other workflow manager as they are designed precisely for the task you are describing.

You can write a simple script to read in the bam files, and execute the cufflinks command. Using the -with-docker flag will tell it to run it inside the container where your tools are.

Something like:

#!/usr/bin nextflow

params.bams = "/path/to/bams/*.bam"
Channel 
     .frompath( params.bams )
     .set{ bams }

params.genome = "/path/to/hg19.fa"
genome_file = file(params.genome)

params.gtf = "path/to/hg19.gtf"
gtf_file = file(params.gtf)

process cufflinks{
     publishDir "Results", mode:'copy'

    input:
    file bam from bams
    file genome from genome_file
    file gtf from gtf_file

    output:
    file "*.gtf" into outputs

    script:
    """
    cufflinks -b $genome -g $gtf -u $bam
    """
}

Should be more than enough to get you up and running there. Nextflow is easy to install and you will not run into sudo problems (assuming you are on a HPC with 700+ bams).